def testCreateDatasourceWithMissingValues(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.missing.txt")
destDir = "out"
datasourceFilename = "ESP6500SI-V2.chr1.snps_indels.head.25.missing.tabix_indexed.txt.gz"
indexColumnNames = "CHROM,POS,POS"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "EA_GTC,DP"
configFilename = os.path.join("out", "esp_coverage.missing.config")
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename, dataSourceType, dataSourceName,
dataSourceVersion, dataSourceMatchMode, annotationColumnNames,
DatasourceInstallUtils.getIndexCols(dataSourceType, indexColumnNames))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("data_types", "EA_GTC"), "Float",
"Expected EA_GTC data type is %s but was %s."
% ("Float", configParser.get("data_types", "EA_GTC")))
self.assertEqual(configParser.get("data_types", "DP"), "Integer",
"Expected DP data type is %s but was %s."
% ("Integer", configParser.get("data_types", "DP")))
def testCreateGPTsvConfigFile(self):
configFilename = "out/ccle_by_gp.config"
datasourceFilename = "ccle_results_by_pos.hg19.import.txt"
dataSourceType = "gp_tsv"
dataSourceName = "CCLE_By_GP"
dataSourceVersion = "09292010"
genomicPositionColumnNames = "chr,start,end"
datasourceBuilder = GenericTsvDatasourceCreator()
datasourceBuilder._createConfigFile(
configFilename=configFilename,
baseDSFile=datasourceFilename,
ds_name=dataSourceName,
ds_type=dataSourceType,
ds_version=dataSourceVersion,
indexCols=DatasourceInstallUtils.getIndexCols(
"gp_tsv", genomicPositionColumnNames))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"),
"general section is missing.")
self.assertTrue(configParser.has_option("general", "type"),
"type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"),
"title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"),
"version option is missing in general section.")
self.assertTrue(
configParser.has_option("general", "genomic_position_cols"),
"genomic_position_cols option is missing in general section.")
self.assertEqual(
configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s." %
(dataSourceType, configParser.get("general", "type")))
self.assertEqual(
configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s." %
(datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(
configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s." %
(dataSourceName, configParser.get("general", "title")))
self.assertEqual(
configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s." %
(dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(
configParser.get("general", "genomic_position_cols"),
genomicPositionColumnNames,
"Expected data source genomic_position_cols is %s but was %s." %
(genomicPositionColumnNames,
configParser.get("general", "genomic_position_cols")))
def getGeneTsvConfigFile(self):
configFilename = "out/simple_uniprot.config"
datasourceFilename = "simple_uniprot.out.2011_09.tsv"
dataSourceType = "gene_tsv"
dataSourceName = "UniProt"
dataSourceVersion = "2011_09"
geneColumnName = "gene"
datasourceBuilder = GenericTsvDatasourceCreator()
datasourceBuilder._createConfigFile(
configFilename=configFilename,
baseDSFile=datasourceFilename,
ds_name=dataSourceName,
ds_type=dataSourceType,
ds_version=dataSourceVersion,
indexCols=DatasourceInstallUtils.getIndexCols(
"gene_tsv", geneColumnName))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"),
"general section is missing.")
self.assertTrue(configParser.has_option("general", "type"),
"type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"),
"title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"),
"version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "gene_col"),
"gene_col option is missing in general section.")
self.assertEqual(
configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s." %
(dataSourceType, configParser.get("general", "type")))
self.assertEqual(
configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s." %
(datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(
configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s." %
(dataSourceName, configParser.get("general", "title")))
self.assertEqual(
configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s." %
(dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(
configParser.get("general", "gene_col"), geneColumnName,
"Expected data source gene_col is %s but was %s." %
(geneColumnName, configParser.get("general", "gene_col")))
def testCreateDatasourceWithMissingAnnotationColumns(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.missing.txt")
destDir = "out"
indexColumnNames = "CHROM,POS,POS"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "EA_GTC,DP,ESP_DBSNP"
configFilename = os.path.join("out", "esp_coverage.missing_annotation_cols.config")
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
with self.assertRaises(ValueError):
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename, dataSourceType,
dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames,
DatasourceInstallUtils.getIndexCols(dataSourceType, indexColumnNames))
def testCreateDatasourceWithMissingAnnotationColumns(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.txt")
destDir = "out"
indexColumnNames = "CHROM,POS,POS"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "EA_GTC,DP,ESP_DBSNP"
configFilename = os.path.join("out", "esp_coverage.missing.config")
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
try:
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename, dataSourceType,
dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames,
DatasourceInstallUtils.getIndexCols(dataSourceType, indexColumnNames))
except ValueError:
pass
def testCreateDatasourceWithMissingColumns(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.txt")
destDir = "out"
indexColumnNames = "CHROM,POS,POS"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "EA_GTC,DP"
configFilename = os.path.join("out", "esp_coverage.missing.config")
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
try:
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename,
dataSourceType, dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames,
DatasourceInstallUtils.getIndexCols(dataSourceType, indexColumnNames))
except InputMismatchException:
pass
def testCreateGPTsvConfigFile(self):
configFilename = "out/ccle_by_gp.config"
datasourceFilename = "ccle_results_by_pos.hg19.import.txt"
dataSourceType = "gp_tsv"
dataSourceName = "CCLE_By_GP"
dataSourceVersion = "09292010"
genomicPositionColumnNames = "chr,start,end"
datasourceBuilder = GenericTsvDatasourceCreator()
datasourceBuilder._createConfigFile(configFilename=configFilename, baseDSFile=datasourceFilename,
ds_name=dataSourceName, ds_type=dataSourceType, ds_version=dataSourceVersion,
indexCols=DatasourceInstallUtils.getIndexCols("gp_tsv",
genomicPositionColumnNames))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "genomic_position_cols"),
"genomic_position_cols option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "genomic_position_cols"), genomicPositionColumnNames,
"Expected data source genomic_position_cols is %s but was %s."
% (genomicPositionColumnNames, configParser.get("general", "genomic_position_cols")))
def getGeneTsvConfigFile(self):
configFilename = "out/simple_uniprot.config"
datasourceFilename = "simple_uniprot.out.2011_09.tsv"
dataSourceType = "gene_tsv"
dataSourceName = "UniProt"
dataSourceVersion = "2011_09"
geneColumnName = "gene"
datasourceBuilder = GenericTsvDatasourceCreator()
datasourceBuilder._createConfigFile(configFilename=configFilename, baseDSFile=datasourceFilename,
ds_name=dataSourceName, ds_type=dataSourceType, ds_version=dataSourceVersion,
indexCols=DatasourceInstallUtils.getIndexCols("gene_tsv", geneColumnName))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "gene_col"),
"gene_col option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "gene_col"), geneColumnName,
"Expected data source gene_col is %s but was %s."
% (geneColumnName, configParser.get("general", "gene_col")))
def testCreateDatasource(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.txt")
destDir = "out"
datasourceFilename = "ESP6500SI-V2.chr1.snps_indels.head.25.tabix_indexed.txt.gz"
indexColumnNames = "CHROM,POS,POS,REF,ALT"
columnNames = "CHROM,POS,REF,ALT,DBSNP,EA_AC,AA_AC,TAC,MAF,GTS,EA_GTC,AA_GTC,GTC,DP,FG,GM,AA,AAC,PP,CDP,PH,CP,CG,GL,GS,CA,EXOME_CHIP,GWAS_PUBMED"
configFilename = "out/esp_coverage.config"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "DBSNP,EA_GTC,DP"
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename, dataSourceType,
dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames, DatasourceInstallUtils.getIndexCols(dataSourceType,
indexColumnNames))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_section("data_types"), "data_types section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "column_names"),
"column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "annotation_column_names"),
"annotation_column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "match_mode"),
"match_mode option is missing in general section")
self.assertTrue(configParser.has_option("general", "index_column_names"),
"index_column_names option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "column_names"), columnNames,
"Expected data source column names is %s but was %s."
% (columnNames, configParser.get("general", "column_names")))
self.assertEqual(configParser.get("general", "annotation_column_names"), annotationColumnNames,
"Expected data source annotation column names is %s but was %s."
% (annotationColumnNames, configParser.get("general", "annotation_column_names")))
self.assertEqual(configParser.get("general", "match_mode"), dataSourceMatchMode,
"Expected data source match mode is %s but was %s."
% (dataSourceMatchMode, configParser.get("general", "match_mode")))
self.assertEqual(configParser.get("general", "index_column_names"), indexColumnNames,
"Expected data source index column names is %s but was %s."
% (indexColumnNames, configParser.get("general", "index_column_names")))
self.assertEqual(configParser.get("data_types", "EA_GTC"), "String",
"Expected EA_GTC data type is %s but was %s."
% ("String", configParser.get("data_types", "EA_GTC")))
self.assertEqual(configParser.get("data_types", "DP"), "Integer",
"Expected DP data type is %s but was %s."
% ("Integer", configParser.get("data_types", "DP")))
def testCreateConfigFile(self):
"""
"""
configFilename = os.path.join("out", "esp_coverage.config")
datasourceFilename = "ESP6500SI-V2.coverage.txt.gz"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
indexColumnNames = "Chromosome,Position,Position"
columnNames = "Chromosome,Position,TotalSamplesCovered,AvgSampleReadDepth,TotalEAsamplesCovered,AvgEAsampleReadDepth,TotalAAsamplesCovered,AvgAAsampleReadDepth"
annotationColumnNames = "TotalSamplesCovered,AvgSampleReadDepth,AvgEAsampleReadDepth,TotalAAsamplesCovered,AvgAAsampleReadDepth"
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
datasourceBuilder._createConfigFile(configFilename=configFilename, baseDSFile=datasourceFilename,
ds_type=dataSourceType, ds_name=dataSourceName,
ds_version=dataSourceVersion, column_names=columnNames,
annotation_column_names=annotationColumnNames,
ds_match_mode=dataSourceMatchMode,
indexCols=DatasourceInstallUtils.getIndexCols(dataSourceType,
indexColumnNames))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_section("data_types"), "data_types section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "column_names"),
"column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "annotation_column_names"),
"annotation_column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "match_mode"),
"match_mode option is missing in general section")
self.assertTrue(configParser.has_option("general", "index_column_names"),
"index_column_names option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "column_names"), columnNames,
"Expected data source column names is %s but was %s."
% (columnNames, configParser.get("general", "column_names")))
self.assertEqual(configParser.get("general", "annotation_column_names"), annotationColumnNames,
"Expected data source annotation column names is %s but was %s."
% (annotationColumnNames, configParser.get("general", "annotation_column_names")))
self.assertEqual(configParser.get("general", "match_mode"), dataSourceMatchMode,
"Expected data source match mode is %s but was %s."
% (dataSourceMatchMode, configParser.get("general", "match_mode")))
self.assertEqual(configParser.get("general", "index_column_names"), indexColumnNames,
"Expected data source index column names is %s but was %s."
% (indexColumnNames, configParser.get("general", "index_column_names")))
def testCreateDatasource(self):
"""
"""
dsFile = os.path.join("testdata",
"ESP6500SI-V2.chr1.snps_indels.head.25.txt")
# Never specify "out/"
destDir = "out/create_ds_test/"
if os.path.exists(destDir):
shutil.rmtree(destDir)
os.makedirs(destDir)
datasourceFilename = "ESP6500SI-V2.chr1.snps_indels.head.25.tabix_indexed.txt.gz"
indexColumnNames = "CHROM,POS,POS,REF,ALT"
columnNames = "CHROM,POS,REF,ALT,DBSNP,EA_AC,AA_AC,TAC,MAF,GTS,EA_GTC,AA_GTC,GTC,DP,FG,GM,AA,AAC,PP,CDP,PH,CP,CG,GL,GS,CA,EXOME_CHIP,GWAS_PUBMED"
configFilename = "out/esp_coverage.config"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "DBSNP,EA_GTC,DP"
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
datasourceBuilder.createDatasource(
destDir, dsFile, indexColumnNames, configFilename, dataSourceType,
dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames,
DatasourceInstallUtils.getIndexCols(dataSourceType,
indexColumnNames))
self.assertTrue(os.path.exists(destDir + datasourceFilename))
self.assertTrue(os.path.exists(destDir + datasourceFilename + ".tbi"))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"),
"general section is missing.")
self.assertTrue(configParser.has_section("data_types"),
"data_types section is missing.")
self.assertTrue(configParser.has_option("general", "type"),
"type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"),
"title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"),
"version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "column_names"),
"column_names option is missing in general section.")
self.assertTrue(
configParser.has_option("general", "annotation_column_names"),
"annotation_column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "match_mode"),
"match_mode option is missing in general section")
self.assertTrue(
configParser.has_option("general", "index_column_names"),
"index_column_names option is missing in general section.")
self.assertEqual(
configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s." %
(dataSourceType, configParser.get("general", "type")))
self.assertEqual(
configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s." %
(datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(
configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s." %
(dataSourceName, configParser.get("general", "title")))
self.assertEqual(
configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s." %
(dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(
configParser.get("general", "column_names"), columnNames,
"Expected data source column names is %s but was %s." %
(columnNames, configParser.get("general", "column_names")))
self.assertEqual(
configParser.get("general",
"annotation_column_names"), annotationColumnNames,
"Expected data source annotation column names is %s but was %s." %
(annotationColumnNames,
configParser.get("general", "annotation_column_names")))
self.assertEqual(
configParser.get("general", "match_mode"), dataSourceMatchMode,
"Expected data source match mode is %s but was %s." %
(dataSourceMatchMode, configParser.get("general", "match_mode")))
self.assertEqual(
configParser.get("general",
"index_column_names"), indexColumnNames,
"Expected data source index column names is %s but was %s." %
(indexColumnNames, configParser.get("general",
"index_column_names")))
self.assertEqual(
configParser.get("data_types", "EA_GTC"), "String",
"Expected EA_GTC data type is %s but was %s." %
("String", configParser.get("data_types", "EA_GTC")))
self.assertEqual(
configParser.get("data_types", "DP"), "Integer",
"Expected DP data type is %s but was %s." %
("Integer", configParser.get("data_types", "DP")))
ds = DatasourceFactory.createDatasourceFromConfigParser(
configParser, "out/create_ds_test/")
mut = MutationData(chr="1",
start="69428",
end="69428",
ref_allele="T",
alt_allele="G")
mut2 = ds.annotate_mutation(mut)
self.assertEquals(mut2["ESP_DBSNP"], "dbSNP_134")
self.assertEquals(mut2["ESP_EA_GTC"], "92,129,3203")
self.assertEquals(mut2["ESP_DP"], "110")
def testCreateDatasource(self):
"""
"""
dsFile = os.path.join("testdata", "ESP6500SI-V2.chr1.snps_indels.head.25.txt")
# Never specify "out/"
destDir = "out/create_ds_test/"
if os.path.exists(destDir):
shutil.rmtree(destDir)
os.makedirs(destDir)
datasourceFilename = "ESP6500SI-V2.chr1.snps_indels.head.25.tabix_indexed.txt.gz"
indexColumnNames = "CHROM,POS,POS,REF,ALT"
columnNames = "CHROM,POS,REF,ALT,DBSNP,EA_AC,AA_AC,TAC,MAF,GTS,EA_GTC,AA_GTC,GTC,DP,FG,GM,AA,AAC,PP,CDP,PH,CP,CG,GL,GS,CA,EXOME_CHIP,GWAS_PUBMED"
configFilename = "out/esp_coverage.config"
dataSourceType = "indexed_tsv"
dataSourceName = "ESP"
dataSourceVersion = "6500SI-V2"
dataSourceMatchMode = "overlap"
annotationColumnNames = "DBSNP,EA_GTC,DP"
datasourceBuilder = TabixIndexedTsvDatasourceCreator()
datasourceBuilder.createDatasource(destDir, dsFile, indexColumnNames, configFilename, dataSourceType,
dataSourceName, dataSourceVersion, dataSourceMatchMode,
annotationColumnNames, DatasourceInstallUtils.getIndexCols(dataSourceType,
indexColumnNames))
self.assertTrue(os.path.exists(destDir + datasourceFilename))
self.assertTrue(os.path.exists(destDir + datasourceFilename + ".tbi"))
configParser = ConfigUtils.createConfigParser(configFilename)
self.assertTrue(configParser.has_section("general"), "general section is missing.")
self.assertTrue(configParser.has_section("data_types"), "data_types section is missing.")
self.assertTrue(configParser.has_option("general", "type"), "type option is missing in general section.")
self.assertTrue(configParser.has_option("general", "src_file"),
"src_file option is missing in general section.")
self.assertTrue(configParser.has_option("general", "title"), "title option is missing in general section.")
self.assertTrue(configParser.has_option("general", "version"), "version option is missing in general section.")
self.assertTrue(configParser.has_option("general", "column_names"),
"column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "annotation_column_names"),
"annotation_column_names option is missing in general section.")
self.assertTrue(configParser.has_option("general", "match_mode"),
"match_mode option is missing in general section")
self.assertTrue(configParser.has_option("general", "index_column_names"),
"index_column_names option is missing in general section.")
self.assertEqual(configParser.get("general", "type"), dataSourceType,
"Expected data source type is %s but was %s."
% (dataSourceType, configParser.get("general", "type")))
self.assertEqual(configParser.get("general", "src_file"), datasourceFilename,
"Expected data source src_file is %s but was %s."
% (datasourceFilename, configParser.get("general", "src_file")))
self.assertEqual(configParser.get("general", "title"), dataSourceName,
"Expected data source title is %s but was %s."
% (dataSourceName, configParser.get("general", "title")))
self.assertEqual(configParser.get("general", "version"), dataSourceVersion,
"Expected data source version is %s but was %s."
% (dataSourceVersion, configParser.get("general", "version")))
self.assertEqual(configParser.get("general", "column_names"), columnNames,
"Expected data source column names is %s but was %s."
% (columnNames, configParser.get("general", "column_names")))
self.assertEqual(configParser.get("general", "annotation_column_names"), annotationColumnNames,
"Expected data source annotation column names is %s but was %s."
% (annotationColumnNames, configParser.get("general", "annotation_column_names")))
self.assertEqual(configParser.get("general", "match_mode"), dataSourceMatchMode,
"Expected data source match mode is %s but was %s."
% (dataSourceMatchMode, configParser.get("general", "match_mode")))
self.assertEqual(configParser.get("general", "index_column_names"), indexColumnNames,
"Expected data source index column names is %s but was %s."
% (indexColumnNames, configParser.get("general", "index_column_names")))
self.assertEqual(configParser.get("data_types", "EA_GTC"), "String",
"Expected EA_GTC data type is %s but was %s."
% ("String", configParser.get("data_types", "EA_GTC")))
self.assertEqual(configParser.get("data_types", "DP"), "Integer",
"Expected DP data type is %s but was %s."
% ("Integer", configParser.get("data_types", "DP")))
ds = DatasourceFactory.createDatasourceFromConfigParser(configParser, "out/create_ds_test/")
mut = MutationData(chr="1", start="69428", end="69428", ref_allele="T", alt_allele="G")
mut2 = ds.annotate_mutation(mut)
self.assertEquals(mut2["ESP_DBSNP"], "dbSNP_134")
self.assertEquals(mut2["ESP_EA_GTC"], "92,129,3203")
self.assertEquals(mut2["ESP_DP"], "110")
